Reloading scripts from a bootstrap script
I found this in the source code. 

https://gitorious.org/blenderprojects/blender/commit/49c90bd

static int script_reload_exec(bContext *C, wmOperator *op)
{
#ifndef DISABLE_PYTHON
    BPY_eval_string(C, "__import__('bpy').utils.load_scripts(reload_scripts=True)");

    return OPERATOR_FINISHED;
#endif
    return OPERATOR_CANCELLED;
}


So I call this in python and it works.

bpy.utils.load_scripts(reload_scripts=True)